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- PDB-1e2i: The nucleoside binding site of Herpes simplex type 1 thymidine ki... -

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Basic information

Entry
Database: PDB / ID: 1e2i
TitleThe nucleoside binding site of Herpes simplex type 1 thymidine kinase analyzed by X-ray crystallography
ComponentsTHYMIDINE KINASE
KeywordsTRANSFERASE / ADENINE ANALOG / ENZYME-PRODRUG GENE THERAPY / NUCLEOSIDE- BINDING / THYMIDINE KINASE
Function / homology
Function and homology information


TMP biosynthetic process / thymidine kinase / thymidine kinase activity / DNA biosynthetic process / ATP binding
Similarity search - Function
Herpesvirus thymidine kinase / Thymidine kinase from herpesvirus / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
9-HYDROXYPROPYLADENINE, S-ISOMER / 9-HYDROXYPROPYLADENINE, R-ISOMER / Thymidine kinase / Thymidine kinase
Similarity search - Component
Biological speciesHERPES SIMPLEX VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsVogt, J. / Scapozza, L. / Schulz, G.E.
Citation
Journal: Proteins / Year: 2000
Title: Nucleoside Binding Site of Herpes Simplex Type 1 Thymidine Kinase Analyzed by X-Ray Crystallography
Authors: Vogt, J. / Perozzo, R. / Pautsch, A. / Prota, A. / Schelling, P. / Pilger, B. / Folkers, G. / Scapozza, L. / Schulz, G.E.
#1: Journal: FEBS Lett. / Year: 1995
Title: The Three-Dimensional Structure of Thymidine Kinase from Herpes Simplex Virus Type 1
Authors: Wild, K. / Bohner, T. / Aubry, A. / Folkers, G. / Schulz, G.E.
#2: Journal: Nat.Struct.Biol. / Year: 1995
Title: Crystal Structures of the Thymidine Kinase from Herpes Simplex Virus Type-1 in Complex with Deoxythymidine and Ganciclovir
Authors: Brown, D.G. / Visse, R. / Sandhu, G. / Davies, A. / Rizkallah, P.J. / Melitz, C. / Summers, W.C. / Sanderson, M.R.
History
DepositionMay 23, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_special_symmetry / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: THYMIDINE KINASE
B: THYMIDINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,5238
Polymers71,5582
Non-polymers9656
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5760 Å2
ΔGint-46.89 kcal/mol
Surface area23340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.000, 116.900, 108.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-2090-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.92993, -0.31266, -0.19356), (-0.31911, 0.42456, 0.8473), (-0.18274, 0.8497, -0.49459)
Vector: 74.60172, 22.24124, -9.82225)
DetailsTHE STRONG CRYSTAL PACKING GENERATED USING X , 1-Y, -Z GIVESCHAIN A TO CHAIN A (SYMMETRY RELATED) CONTACTS.

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Components

#1: Protein THYMIDINE KINASE


Mass: 35779.086 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HERPES SIMPLEX VIRUS (TYPE 1 / STRAIN 17)
Strain: 17 / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P03176, UniProt: P0DTH5*PLUS, thymidine kinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-APS / 9-HYDROXYPROPYLADENINE, S-ISOMER


Mass: 193.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H11N5O
#4: Chemical ChemComp-ARP / 9-HYDROXYPROPYLADENINE, R-ISOMER


Mass: 193.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H11N5O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.64 %
Crystal growpH: 7.5 / Details: LITHIUM SULFATE, HEPES, DTT, pH 7.50
Crystal grow
*PLUS
Temperature: 23 ℃ / Method: vapor diffusion, sitting drop / PH range low: 8 / PH range high: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
125 mg/mlprotein1drop
20.9-1.2 M1reservoirLi2SO4
31 mMdithiothreitol1reservoir
40.1 MHEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8468
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 12, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8468 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 54250 / % possible obs: 96 % / Redundancy: 3.3 % / Biso Wilson estimate: 29.8 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 12.5
Reflection shellResolution: 1.9→2 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 2.7 / Rsym value: 0.425 / % possible all: 96
Reflection
*PLUS
Rmerge(I) obs: 0.05

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VTK

1vtk


Resolution: 1.9→20 Å / SU B: 2.4 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.16 / ESU R Free: 0.16
RfactorNum. reflection% reflectionSelection details
Rfree0.273 2713 5 %RANDOM
Rwork0.222 ---
obs-54250 96 %-
Displacement parametersBiso mean: 42 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4682 0 66 221 4969
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.013
X-RAY DIFFRACTIONp_angle_d0.026
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.222
Solvent computation
*PLUS
Displacement parameters
*PLUS

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